Re: [AMBER] running qsub files in a single standalone workstation

From: Nadine Homeyer <>
Date: Wed, 8 May 2019 09:09:28 +0300


in order to use the batch files created by FEW per default in each
calculation folder for a submission of the calculations via the command
shell these files need to be changed into pure shell scripts. It is best
to use the CSH shell, as the template queuing scripts used by FEW are
written for this shell. If for some reason another shell has to be used,
the commands in the queuing scripts have to be manually adapted to the
corresponding commands valid vor the respective shell. Please consult
the literature on how to use the respective shell and the available

If you can use the CSH shell, it should be sufficient to remove the
queuing system and computing architecture specific commands, e.g. the
commands for loading specific modules and the line "echo $HOSTNAME".
This can be done directly in the batch template files (e.g. equi.pbs or
prod.pbs in the input_info folder) used for calculation setup with FEW.
The lines starting with #PBS can be kept, since lines starting with "#"
are treated as comments.

In order to use the created and files for
automated job submission the commands for submission of calculations to
a queuing system like "qsub" have to be removed. In addition, it needs
to be ensured that all batch files in the calculation folders are

Kind regards,


Am 08.05.2019 um 08:32 schrieb ali akbar:
> Hi,
> Thanks for your reply. I am trying to calculate ligand-receptor binding
> energy using FEW program (tutorial A24). The qsub files I have obtained are
> and I was wondering how can I get work these files
> for MD simulation using standalone workstation system and how should I
> change my *.pbs files?
> Best Regards,
> Ali Akbar
> _______________________________________________
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Received on Tue May 07 2019 - 23:30:02 PDT
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